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Publications
1st year
1. S.J. de Vries, A.D.J. van Dijk and A.M.J.J. Bonvin "WHISCY: WHat Information does Surface Conservation Yield? Application to data-driven docking." Proteins: Struc. Funct. & Bioinformatics, 63, 479-489 (2006).
2. A.D.J. van Dijk, S.J. de Vries, C. Dominguez, H. Chen, H.-X. Zhou and A.M.J.J. Bonvin "Data-driven docking: HADDOCKs adventures in CAPRI." Proteins: Struc. Funct. & Bioinformatics, 60, 232-238 (2005).
3. L. Rutten, J. Geurtsen, W. Lambert, J.J. Smolenaers, A.M.J.J. Bonvin, A. de Haan, P. van der Ley, M.R. Egmond, P. Gros and J. Tommassen. "Crystal structure and catalytic mechanism of the LPS 3-O-deacylase PagL from Pseudomonas aeruginosa." Proc. Natl. Acad. Sci., 103 7071-7076-244 (2006).
4. Bertini, M. Fragai, A. Giachetti, C. Luchinat, M. Maletta, G. Parigi and Kwon Joo Yeo. “Combining in-silico tools and NMR data to validate protein-ligand structural models: Application to matrix metalloproteinases”. J. Med. Chem. 2005, 48, 7544-7559.
2nd year
5. van Dijk AD, Boelens R, Bonvin AM. Data-driven docking for the study of biomolecular complexes. FEBS J. 2005 Jan;272(2):293-312. Review.
6. van Dijk AD, Fushman D, Bonvin AM. Various strategies of using residual dipolar couplings in NMR-driven protein docking: application to Lys48-linked di-ubiquitin and validation against 15N-relaxation data. Proteins. 2005 Aug 15;60(3):367-81.
7. Volkov AN, Ferrari D, Worrall JA, Bonvin AM, Ubbink M. The orientations of cytochrome c in the highly dynamic complex with cytochrome b5 visualized by NMR and docking using HADDOCK. Protein Sci. 2005 Mar;14(3):799-811.
8. van Dijk AD, Bonvin AM. Solvated docking: introducing water into the modelling of biomolecular complexes. Bioinformatics. 2006 Oct 1;22(19):2340-7.
9. van Dijk AD, Kaptein R, Boelens R, Bonvin AM. Combining NMR relaxation with chemical shift perturbation data to drive protein-protein docking. J Biomol NMR. 2006 Apr;34(4):237-44.
10. van Dijk M, van Dijk AD, Hsu V, Boelens R, Bonvin AM. Information-driven protein-DNA docking using HADDOCK: it is a matter of flexibility. Nucleic Acids Res. 2006 Jul 4;34(11):3317-25.
11. Bonvin AM. Flexible protein-protein docking. Curr Opin Struct Biol. 2006 Apr;16(2):194-200. Review.
12. de Vries SJ, Bonvin AM. Intramolecular surface contacts contain information about protein-protein interface regions. Bioinformatics. 2006 Sep 1;22(17):2094-8.
13. Mittag, T. et al., JACS, 2006, 128, 9844-9848
14. Manger M, Scheck M, Prinz H, von Kries JP, Langer T, Saxena K, Schwalbe H, Fürstner A, Rademann J, Waldmann H., ChemBioChem, 2005, 6, 1749-1753.
15. Nören-Müller A, Reis-Corrêa I, Prinz H, Rosenbaum C, Saxena K, Schwalbe H, Vestweber D, Cagna G, Schunk S, Schwarz O, Schiewe H, Waldmann H., PNAS, 2006, 103, 10606-11
3rd year
16. Bertini I., Felli I., Luchinat C., Parigi G., Pierattelli R. ChemBioChem, 2007, 12, 1422-1429. (DL2)
17. Ulrich Schieborr, Martin Vogtherr, Bettina Elshorst, Marco Betz, Susanne Grimme, Barbara Pescatore, Thomas Langer, Krishna Saxena, Harald Schwalbe (2005), How Much NMR Data Is Required To Determine a Protein-Ligand Complex Structure?, ChemBioChem 6, 1891 – 1898 (DL4)
18. Andrea Nören-Müller, Wolfram Wilk, Krishna Saxena, Harald Schwalbe, Markus Kaiser, Herbert Waldmann, Angew Chem Int Ed Engl. 2008;47(32):5973-7. (DL4, DL8)
19. Calderone V., Fragai M., Luchinat C., Nativi C., Richichi B., Roelens S. ChemMedChem, 2006, 1, 598-601. (DL6)
20. Bertini I., Fragai M., Luchinat C., Talluri E. Angew. Chem. Int. Ed. 2008 (DL6)
21. Bertini I., Fragai M., Giachetti A., Luchinat C., Maletta M., Parigi G., Yeo K.J. Combining in silico tools and NMR data to validate protein-ligand structural models: application to matrix metalloproteinases. J. Med. Chem. 2005, 48, 7544-59 (DL7)
22. Bertini I., Calderone V., Fragai M. Giachetti A., Loconte M., Luchinat C., Maletta M., Nativi C., Yeo K.J., Exploring the Subtleties of Drug-Receptor Interactions: The Case of Matrix Metalloproteinases, J. Am. Chem. Soc. 2007, 129, 2466-2475. (DL7)
23. Assfalg M., Bertini I., Del Conte, Andrea Giachetti, Paola Turano, Biochemistry, 2007, 46, 6238. (DL8)
24. Arendt Y., Bhaumik A., Del Conte R., Luchinat C., Mori M., Porcu M. ChemMedChem, 2007, 2, 1648-1654. (DL8)
25. S.J. de Vries, A.D.J. van Dijk, M. Krzeminski, M. van Dijk, A. Thureau, V. Hsu, T. Wassenaar and A.M.J.J. Bonvin (207).HADDOCK versus HADDOCK: New features and performance of HADDOCK2.0 on the CAPRI targets. Proteins: Struc. Funct. & Bioinformatic 69, 726-733. (DL9)
26. Bertini I., Gupta Y.K., Luchinat C., Parigi C., Peana M., Sgheri L., Yuan J. J. Am. Chem. Soc. 2007, 129, 12786-12794. (DL9)
27. Shannon M. Harper, Hans Wienk, Rainer W. Wechselberger, Holger Rehmann, Johannes L. Bos, Rolf Boelens (J. Biol.Chem. 2008 283(10) 6501-6508) (DL10)
28. Hans Wienk, Shannon M. Harper, Rainer W. Wechselberger, Holger Rehmann, Johannes L. Bos, and Rolf Boelens (Manuscript in preparation) (DL10)
29. Nesi A., Fragai M. ChemBioChem, 2007, 8, 1367-1369. (DL10)
30. Bertini I., Fragai M., Luchinat C., Talluri E. In Preparation (DL13)
31. Hans Hombauer, David Weismann, Ingrid Mudrak, Claudia Stanzel, Thomas Fellner, Daniel H. Lackner, Egon Ogris, Generation of Active Protein Phosphatase 2A Is Coupled to Holoenzyme Assembly, 2007, PloS Biology, 5, e155, 1355-65
NDDP is a STREP Funded by the 6th Research Framework Program of the European Union
(Contract: LSHG-CT-2004-512077)